Usage

Warning

As of FMRIPREP 1.0.12, the software includes a tracking system
to report usage statistics and errors. Users can opt-out using
the --notrack command line argument.

Execution and the BIDS format

The fmriprep workflow takes as principal input the path of the dataset
that is to be processed.
The input dataset is required to be in valid :abbr:`BIDS (Brain Imaging Data
Structure)` format, and it must include at least one T1w structural image and
(unless disabled with a flag) a BOLD series.
We highly recommend that you validate your dataset with the free, online
BIDS Validator.

The exact command to run fmriprep depends on the Installation_ method.
The common parts of the command follow the BIDS-Apps definition.
Example:

The docker wrapper CLI

Debugging

Logs and crashfiles are outputted into the
<output dir>/fmriprep/sub-<participant_label>/log directory.
Information on how to customize and understand these files can be found on the
nipype debugging
page.

If you have a problem or would like to ask a question about how to use fmriprep,
please submit a question to NeuroStars.org with an fmriprep tag.
NeuroStars.org is a platform similar to StackOverflow but dedicated to neuroinformatics.